% This file was created with JabRef 2.9.2.
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@string{lncs={LNCS}}
@string{tcs = {TCS}}
@string{entcs = {ENTCS}}

@INPROCEEDINGS{Basso-Blandin2012,
  author = {Adrien Basso-Blandin and Franck Delaplace},
  title = {GUBS, a behavior-based language for open system dedicated to synthetic
	biology},
  booktitle = {MeCBIC},
  year = {2012},
  pages = {29-47},
  bibsource = {DBLP, http://dblp.uni-trier.de},
  crossref = {DBLP:journals/corr/abs-1211-3476},
  ee = {http://dx.doi.org/10.4204/EPTCS.100.3}
}

@ARTICLE{AbdullaCJT00,
  author = {Parosh Aziz Abdulla and Karlis Cerans and Bengt Jonsson and Yih-Kuen
	Tsay},
  title = {Algorithmic Analysis of Programs with Well Quasi-ordered Domains},
  journal = {Information and Computation},
  year = {2000},
  volume = {160},
  pages = {109-127},
  number = {1-2},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}

@ARTICLE{afshari,
  author = {Afshari, Cynthia A. and Hamadeh, Hisham K. and Bushel Pierre R.},
  title = {The evolution of bioinformatics in toxicology: advancing toxicogenomics},
  journal = {Toxicological Sciences},
  year = {2011},
  volume = {120},
  pages = {225-237},
  number = {1}
}

@ARTICLE{Basso-Blandin2013,
  author = {Adrien Basso-Blandin and Franck Delaplace},
  title = {GUBS, a Behaviour-Based Language for Design in Synthetic Biology},
  journal = {Sci. Ann. Comp. Sci.},
  year = {2013},
  volume = {23},
  pages = {1-38},
  number = {1},
  bibsource = {DBLP, http://dblp.uni-trier.de},
  ee = {http://dx.doi.org/10.7561/SACS.2013.1.1},
  owner = {Franck},
  timestamp = {2014.01.03}
}

@ARTICLE{Beal2011,
  author = {Beal, Jacob and Lu, Ting and Weiss, Ron},
  title = {{Automatic Compilation from High-Level Biologically-Oriented Programming
	Language to Genetic Regulatory Networks}},
  journal = {PLoS ONE},
  year = {2011},
  volume = {6},
  pages = {e22490},
  number = {8},
  doi = {10.1371/journal.pone.0022490},
  editor = {Ben-Jacob, Eshel},
  file = {:C$\backslash$:/Users/Franck/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Beal, Lu, Weiss - 2011 - Automatic Compilation from High-Level Biologically-Oriented Programming Language to Genetic Regulatory Networks.pdf:pdf},
  issn = {1932-6203},
  url = {http://dx.plos.org/10.1371/journal.pone.0022490}
}

@ARTICLE{Bilitchenko2011,
  author = {Bilitchenko, Lesia and Liu, Adam and Cheung, Sherine and Weeding,
	Emma and Xia, Bing and Leguia, Mariana and Anderson, J. Christopher
	and Densmore, Douglas},
  title = {{Eugene--a domain specific language for specifying and constraining
	synthetic biological parts, devices, and systems.}},
  journal = {PloS one},
  year = {2011},
  volume = {6},
  pages = {e18882},
  number = {4},
  abstract = {Synthetic biological systems are currently created by an ad-hoc, iterative
	process of specification, design, and assembly. These systems would
	greatly benefit from a more formalized and rigorous specification
	of the desired system components as well as constraints on their
	composition. Therefore, the creation of robust and efficient design
	flows and tools is imperative. We present a human readable language
	(Eugene) that allows for the specification of synthetic biological
	designs based on biological parts, as well as provides a very expressive
	constraint system to drive the automatic creation of composite Parts
	(Devices) from a collection of individual Parts.},
  doi = {10.1371/journal.pone.0018882},
  file = {:C$\backslash$:/Users/Franck/Dropbox/My Bibliography/Bilitchenko et al. - 2011 - Eugene--a domain specific language for specifying and constraining synthetic biological parts, devices, and systems.pdf:pdf},
  issn = {1932-6203},
  pmid = {21559524},
  url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3084710\&tool=pmcentrez\&rendertype=abstract}
}

@ARTICLE{DBLP:journals/ijfcs/BrijderEMR11,
  author = {Robert Brijder and Andrzej Ehrenfeucht and Michael G. Main and Grzegorz
	Rozenberg},
  title = {A Tour of reaction Systems},
  journal = { Journal of Foundations of Computer Science},
  year = {2011},
  volume = {22},
  pages = {1499-1517},
  number = {7},
  bibsource = {DBLP, http://dblp.uni-trier.de},
  ee = {http://dx.doi.org/10.1142/S0129054111008842}
}

@ARTICLE{journals/tcsb/Cardelli05,
  author = {Cardelli, Luca},
  title = {Abstract Machines of Systems Biology.},
  journal = {Transactions on Computational Systems Biology},
  year = {2005},
  volume = {3737},
  pages = {145-168},
  added-at = {2005-12-22T00:00:00.000+0100},
  biburl = {http://www.bibsonomy.org/bibtex/20e3ebf1e17c6b782a59c09d0481fc406/dblp},
  date = {2005-12-22},
  description = {dblp},
  editor = {Priami, Corrado and Merelli, Emanuela and Gonzalez, Pedro Pablo and
	Omicini, Andrea},
  ee = {http://dx.doi.org/10.1007/11599128_10},
  interhash = {2848be2cdd43ed54ccd19f1789eecc1c},
  intrahash = {0e3ebf1e17c6b782a59c09d0481fc406},
  isbn = {3-540-30883-0},
  keywords = {dblp},
  publisher = {Springer},
  series = lncs,
  timestamp = {2005-12-22T00:00:00.000+0100},
  url = {http://dblp.uni-trier.de/db/journals/tcsb/tcsb3.html#Cardelli05}
}

@INCOLLECTION{CardelliP09,
  author = {Cardelli, Luca and Priami, Corrado},
  title = {Visualization in process algebra models of biological systems.},
  booktitle = {The Fourth Paradigm},
  publisher = {Microsoft Research},
  year = {2009},
  editor = {Hey, Tony and Tansley, Stewart and Tolle, Kristin M.},
  pages = {99-105},
  added-at = {2011-09-22T00:00:00.000+0200},
  biburl = {http://www.bibsonomy.org/bibtex/20fc143882c83b3491ee5002153805ca3/dblp},
  ee = {http://research.microsoft.com/en-us/collaboration/fourthparadigm/4th_paradigm_book_part2_cardelli_priami.pdf},
  interhash = {f8cdc5cb772c91659a0405a009e3fb4b},
  intrahash = {0fc143882c83b3491ee5002153805ca3},
  isbn = {978-0982544204},
  keywords = {dblp},
  timestamp = {2011-09-22T00:00:00.000+0200},
  url = {http://dblp.uni-trier.de/db/books/collections/4paradigm2009.html#CardelliP09}
}

@ARTICLE{Czar2009,
  author = {Czar, Michael J. and Cai, Yizhi and Peccoud, Jean},
  title = {{Writing DNA with GenoCAD.}},
  journal = {Nucleic acids research},
  year = {2009},
  volume = {37},
  pages = {W40--7},
  number = {Web Server issue},
  abstract = {Chemical synthesis of custom DNA made to order calls for software
	streamlining the design of synthetic DNA sequences. GenoCAD (www.genocad.org)
	is a free web-based application to design protein expression vectors,
	artificial gene networks and other genetic constructs composed of
	multiple functional blocks called genetic parts. By capturing design
	strategies in grammatical models of DNA sequences, GenoCAD guides
	the user through the design process. By successively clicking on
	icons representing structural features or actual genetic parts, complex
	constructs composed of dozens of functional blocks can be designed
	in a matter of minutes. GenoCAD automatically derives the construct
	sequence from its comprehensive libraries of genetic parts. Upon
	completion of the design process, users can download the sequence
	for synthesis or further analysis. Users who elect to create a personal
	account on the system can customize their workspace by creating their
	own parts libraries, adding new parts to the libraries, or reusing
	designs to quickly generate sets of related constructs.},
  doi = {10.1093/nar/gkp361},
  file = {:C$\backslash$:/Users/Franck/Dropbox/My Bibliography/Czar, Cai, Peccoud - 2009 - Writing DNA with GenoCAD.pdf:pdf},
  issn = {1362-4962},
  keywords = {Base Sequence,DNA,DNA: chemical synthesis,DNA: chemistry,Genes, Synthetic,Genetic
	Engineering,Software,User-Computer Interface},
  pmid = {19429897},
  url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2703884\&tool=pmcentrez\&rendertype=abstract}
}

@ARTICLE{DBLP:journals/tcs/DanosL04,
  author = {Vincent Danos and Cosimo Laneve},
  title = {Formal molecular biology},
  journal = tcs,
  year = {2004},
  volume = {325},
  pages = {69-110},
  number = {1},
  bibsource = {DBLP, http://dblp.uni-trier.de},
  ee = {http://dx.doi.org/10.1016/j.tcs.2004.03.065}
}

@INCOLLECTION{DeCristofaro2008,
  author = {DeCristofaro, MarcF. and Daniels, KellyeK.},
  title = {Toxicogenomics in Biomarker Discovery},
  booktitle = {Essential Concepts in Toxicogenomics},
  publisher = {Humana Press},
  year = {2008},
  editor = {Mendrick, DonnaL. and Mattes, WilliamB.},
  volume = {460},
  series = {Methods in Molecular Biology™},
  pages = {185-194},
  doi = {10.1007/978-1-60327-048-9_9},
  isbn = {978-1-58829-638-2},
  keywords = {biomarker; blood; gene expression; heart; kidney; molecular profiling;
	toxicogenomics; transcriptomics},
  owner = {Franck},
  timestamp = {2014.01.02},
  url = {http://dx.doi.org/10.1007/978-1-60327-048-9_9}
}

@ARTICLE{Ehrenfeucht2007,
  author = {Andrzej Ehrenfeucht and Grzegorz Rozenberg},
  title = {Events and modules in reaction systems},
  journal = tcs,
  year = {2007},
  volume = {376},
  pages = {3-16},
  number = {1-2},
  bibsource = {DBLP, http://dblp.uni-trier.de},
  ee = {http://dx.doi.org/10.1016/j.tcs.2007.01.008}
}

@ARTICLE{emerson,
  author = {E.Allen Emerson and Edmund M. Clarke},
  title = {Using branching time temporal logic to synthesize synchronization
	skeletons },
  journal = {Science of Comp. Programming },
  year = {1982},
  volume = {2},
  pages = {241 - 266},
  number = {3}
}

@ARTICLE{FinkelS01,
  author = {Alain Finkel and Philippe Schnoebelen},
  title = {Well-structured transition systems everywhere!},
  journal = tcs,
  year = {2001},
  volume = {256},
  pages = {63-92},
  number = {1-2},
  bibsource = {DBLP, http://dblp.uni-trier.de},
  ee = {http://dx.doi.org/10.1016/S0304-3975(00)00102-X}
}

@ARTICLE{Foster2007,
  author = {Foster, William R and Chen, Shen-Jue and He, Aiqing and Truong, Amy
	and Bhaskaran, Vasanthi and Nelson, David M and Dambach, Donna M
	and Lehman-McKeeman, Lois D and Car, Bruce D},
  title = {{A retrospective analysis of toxicogenomics in the safety assessment
	of drug candidates.}},
  journal = {Toxicologic pathology},
  year = {2007},
  volume = {35},
  pages = {621--35},
  number = {5},
  month = aug,
  abstract = {Toxicogenomics is considered a valuable tool for reducing pharmaceutical
	candidate attrition by facilitating earlier identification, prediction
	and understanding of toxicities. A retrospective evaluation of 3
	years of routine transcriptional profiling in non-clinical safety
	studies was undertaken to assess the utility of toxicogenomics in
	drug safety assessment. Based on the analysis of studies with 33
	compounds, marked global transcriptional changes (> 4\% transcripts
	at p < 0.01) were shown to be a robust biomarker for dosages considered
	to be toxic . In general, there was an inconsistent correlation between
	transcription and histopathology, most likely due to differences
	in sensitivity to focal microscopic lesions, to secondary effects,
	and to events that precede structural tissue changes. For 60\% of
	toxicities investigated with multiple time-point data, transcriptional
	changes were observed prior to changes in traditional study endpoints.
	Candidate transcriptional markers of pharmacologic effects were detected
	in 40\% of targets profiled. Mechanistic classification of toxicity
	was obtained for 30\% of targets. Furthermore, data comparison to
	compendia of transcriptional changes provided assessments of the
	specificity of transcriptional responses. Overall, our experience
	suggests that toxicogenomics has contributed to a greater understanding
	of mechanisms of toxicity and to reducing drug attrition by empiric
	analysis where safety assessment combines toxicogenomic and traditional
	evaluations.},
  doi = {10.1080/01926230701419063},
  file = {:C$\backslash$:/Users/Franck/Dropbox/My Bibliography/Toxicol Pathol-2007-Foster-621-35.pdf:pdf},
  issn = {0192-6233},
  keywords = {Animals,Biological Markers,Dose-Response Relationship, Drug,Drug-Related
	Side Effects and Adverse Reactions,Gene Expression Profiling,Humans,Retrospective
	Studies,Risk Assessment,Safety,Toxicogenetics},
  mendeley-groups = {Articles/article-toxico},
  owner = {Franck},
  pmid = {17654404},
  timestamp = {2014.01.03},
  url = {http://www.ncbi.nlm.nih.gov/pubmed/17654404}
}

@BOOK{DBLP:series/eatcs/Jensen92,
  title = {Coloured Petri Nets - Basic Concepts, Analysis Methods and Practical
	Use - Volume 1},
  publisher = {Springer},
  year = {1992},
  author = {Kurt Jensen},
  pages = {I-X, 1-236},
  series = {EATCS Monographs on TCS},
  bibsource = {DBLP, http://dblp.uni-trier.de},
  ee = {http://dx.doi.org/10.1007/978-3-662-06289-0},
  isbn = {978-3-662-06291-3, 978-3-662-06289-0}
}

@ARTICLE{kavlock,
  author = {Kavlock, Robert J. and Ankley, Gerald and Blancato, Jerry and Breen,
	Michael and Conolly, Rory and Dix, David and Houck, Keith and Hubal,
	Elaine and Judson, Richard and Rabinowitz, James and Richard, Ann
	and Setzer, Woodrow and Shah, Imran and Villeneuve, Daniel and Weber,
	Eric},
  title = {Computational toxicology--a state of the science mini review},
  journal = {Toxicological Sciences},
  year = {2008},
  volume = {103},
  pages = {14-27},
  number = {1}
}

@INCOLLECTION{MadhuKrithi,
  author = {Madhu, Mutyam and Krithivasan, Kamala},
  title = {A Survey of Some Variants of P Systems},
  booktitle = {Membrane Computing},
  publisher = {Springer Berlin Heidelberg},
  year = {2003},
  editor = {PĂun, Gheorghe and Rozenberg, Grzegorz and Salomaa, Arto and Zandron,
	Claudio},
  volume = {2597},
  series = lncs,
  pages = {360-370},
  doi = {10.1007/3-540-36490-0_24},
  isbn = {978-3-540-00611-4},
  language = {English},
  url = {http://dx.doi.org/10.1007/3-540-36490-0_24}
}

@ARTICLE{computational,
  author = {Materi, Wayne and Wishart, David S.},
  title = {{Computational systems biology in drug discovery and development:
	methods and applications}},
  journal = {Drug Discovery Today},
  year = {2007},
  volume = {12},
  pages = {295--303},
  number = {7-8},
  abstract = {{ Computational systems biology is an emerging field in biological
	simulation that attempts to model or simulate intra- and intercellular
	events using data gathered from genomic, proteomic or metabolomic
	experiments. The need to model complex temporal and spatiotemporal
	processes at many different scales has led to the emergence of numerous
	techniques, including systems of differential equations, Petri nets,
	cellular automata simulators, agent-based models and pi calculus.
	This review provides a brief summary and an assessment of most of
	these approaches. It also provides examples of how these methods
	are being used to facilitate drug discovery and development. }},
  address = {National Research Council, National Institute for Nanotechnology
	(NINT) Edmonton, Alberta, Canada T6G 2E8.},
  doi = {10.1016/j.drudis.2007.02.013},
  issn = {13596446},
  keywords = {rev},
  pmid = {17395089},
  posted-at = {2011-11-12 01:25:57},
  priority = {2},
  url = {http://dx.doi.org/10.1016/j.drudis.2007.02.013}
}

@ARTICLE{toxicogenomics,
  author = {Nuwaysir, EF and Bittner, M and Trent, J and Barrett, JC and Afshari,
	CA},
  title = {Microarrays and toxicology: the advent of toxicogenomics},
  journal = {Molecular Carcinogenesis},
  year = { 1999},
  volume = {24},
  pages = {153-159},
  number = {3}
}

@ARTICLE{DBLP:journals/ijfcs/PaunPRS11,
  author = {Andrei Paun and Mihaela Paun and Alfonso Rodr\'{\i}guez-Pat{\'o}n
	and Manuela Sidoroff},
  title = {P Systems with proteins on Membranes: a Survey.},
  journal = {International Journal of Foundations of Computer Science},
  year = {2011},
  volume = {22},
  pages = {39-53},
  number = {1},
  bibsource = {DBLP, http://dblp.uni-trier.de},
  ee = {http://dx.doi.org/10.1142/S0129054111007812}
}

@ARTICLE{Pennie2000,
  author = {Pennie, WD and Tugwood, JD},
  title = {{The principles and practice of toxicogenomics: applications and
	opportunities}},
  journal = {Toxicological pathology},
  year = {2000},
  volume = {283},
  pages = {277--283},
  owner = {Franck},
  timestamp = {2014.01.02},
  url = {http://toxsci.oxfordjournals.org/content/54/2/277.short}
}

@ARTICLE{pinney,
  author = {Pinney, J. W. and Westhead, D. R. and McConkey, G. A.},
  title = {{Petri Net representations in systems biology.}},
  journal = {Biochemical Society Transactions},
  year = {2003},
  volume = {31},
  pages = {1513--1515},
  number = {Pt 6},
  abstract = {{The mathematical structures known as Petri Nets have recently become
	the focus of much research effort in both the structural and quantitative
	analysis of all kinds of biological networks. This review provides
	a very brief summary of these interesting new research directions.}},
  address = {Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT,
	U.K. john@bioinformatics.leeds.ac.uk},
  citeulike-article-id = {273},
  citeulike-linkout-0 = {http://view.ncbi.nlm.nih.gov/pubmed/14641101},
  citeulike-linkout-1 = {http://www.hubmed.org/display.cgi?uids=14641101},
  issn = {0300-5127},
  keywords = {biology, net, petri, sysbio},
  pmid = {14641101},
  posted-at = {2008-01-27 19:38:47},
  priority = {2},
  url = {http://view.ncbi.nlm.nih.gov/pubmed/14641101}
}

@ARTICLE{Purnick2009,
  author = {Purnick, Priscilla E M and Weiss, Ron},
  title = {{The second wave of synthetic biology: from modules to systems.}},
  journal = {Nature reviews. Molecular cell biology},
  year = {2009},
  volume = {10},
  pages = {410--22},
  number = {6},
  abstract = {Synthetic biology is a research field that combines the investigative
	nature of biology with the constructive nature of engineering. Efforts
	in synthetic biology have largely focused on the creation and perfection
	of genetic devices and small modules that are constructed from these
	devices. But to view cells as true 'programmable' entities, it is
	now essential to develop effective strategies for assembling devices
	and modules into intricate, customizable larger scale systems. The
	ability to create such systems will result in innovative approaches
	to a wide range of applications, such as bioremediation, sustainable
	energy production and biomedical therapies.},
  doi = {10.1038/nrm2698},
  file = {:C$\backslash$:/Users/Franck/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Purnick, Weiss - 2009 - The second wave of synthetic biology from modules to systems.pdf:pdf},
  issn = {1471-0080},
  keywords = {bsao},
  mendeley-tags = {bsao},
  pmid = {19461664},
  shorttitle = {Nat Rev Mol Cell Biol},
  url = {http://www.ncbi.nlm.nih.gov/pubmed/19461664}
}

@ARTICLE{toxicology,
  author = {Schmidt, Markus and Pei, Lei},
  title = {Synthetic toxicology: where engineering meets biology and toxicology},
  journal = {Toxicological sciences : an official journal of the Society of Toxicology},
  year = {2011},
  volume = {Suppl. 1},
  pages = {S204-24},
  number = {120}
}

@ARTICLE{synthetic,
  author = {Serrano, Luis},
  title = {Synthetic biology: promises and challenges},
  journal = {Molecular Systems Biology},
  year = {2007},
  volume = {3},
  number = {158}
}



@article{DBLP:journals/tcs/CeroneM99,
  author    = {Antonio Cerone and
               Andrea Maggiolo-Schettini},
  title     = {Time-Based Expressivity of Time Petri Nets for System Specification},
  journal   = tcs,
  volume    = {216},
  number    = {1-2},
  year      = {1999},
  pages     = {1-53},
  ee        = {http://dx.doi.org/10.1016/S0304-3975(98)00008-5},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}


@ARTICLE{DBLP:journals/entcs/ThanhKP02,
  author = {C{\'e}cile Bui Thanh and Hanna Klaudel and Franck Pommereau},
  title = {Petri nets with causal time for system verification},
  journal = entcs,
  year = {2002},
  volume = {68},
  pages = {85-100},
  number = {5},
  bibsource = {DBLP, http://dblp.uni-trier.de},
  ee = {http://dx.doi.org/10.1016/S1571-0661(04)80521-8}
}

@BOOK{Voigt2011,
  title = {Synthetic Biology: Computer Aided Design and DNA Assembly},
  publisher = {Elsevier/Academic Press},
  year = {2011},
  author = {Voigt, C.},
  series = {Academic Press},
  isbn = {9780123851208},
  owner = {Franck},
  timestamp = {2014.01.04},
  url = {http://books.google.fr/books?id=EJXBAXJYC1oC}
}

@ARTICLE{Waters2004,
  author = {Waters, Michael D and Fostel, Jennifer M},
  title = {{Toxicogenomics and systems toxicology: aims and prospects.}},
  journal = {Nature reviews. Genetics},
  year = {2004},
  volume = {5},
  pages = {936--48},
  number = {12},
  month = dec,
  abstract = {Toxicogenomics combines transcript, protein and metabolite profiling
	with conventional toxicology to investigate the interaction between
	genes and environmental stress in disease causation. The patterns
	of altered molecular expression that are caused by specific exposures
	or disease outcomes have revealed how several toxicants act and cause
	disease. Despite these success stories, the field faces noteworthy
	challenges in discriminating the molecular basis of toxicity. We
	argue that toxicology is gradually evolving into a systems toxicology
	that will eventually allow us to describe all the toxicological interactions
	that occur within a living system under stress and use our knowledge
	of toxicogenomic responses in one species to predict the modes-of-action
	of similar agents in other species.},
  doi = {10.1038/nrg1493},
  file = {:C$\backslash$:/Users/Franck/Dropbox/My Bibliography/tox\_ReviewToxicogenomicsNaturedec2004.pdf:pdf},
  issn = {1471-0056},
  keywords = {Animals,Computational Biology,Databases, Factual,Ecology,Forecasting,Gene
	Expression Profiling,Genetic Predisposition to Disease,Humans,Proteomics,Systems
	Theory,Toxicogenetics,Toxicology},
  owner = {Franck},
  pmid = {15573125},
  timestamp = {2014.01.02},
  url = {http://www.ncbi.nlm.nih.gov/pubmed/15573125}
}

@PROCEEDINGS{DBLP:journals/corr/abs-1211-3476,
  title = {Proceedings 6th Workshop on Membrane Computing and Biologically Inspired
	Process Calculi},
  year = {2012},
  editor = {Gabriel Ciobanu},
  volume = {100},
  series = {EPTCS},
  bibsource = {DBLP, http://dblp.uni-trier.de},
  booktitle = {MeCBIC},
  ee = {http://dx.doi.org/10.4204/EPTCS.100}
}


@Article{kripke,
 author = {Saul Kripke},
 title = {Semantical Considerations on Modal Logic},
 journal = {Acta Philosophica Fennica },
 year = {1963},
 volume = {16},
 pages = {83–94},
 }
 
 @book{edmund,
  author    = {Edmund M. Clarke and
               Orna Grumberg and
               Doron Peled},
  title     = {Model checking},
  publisher = {MIT Press},
  year      = {2001},
  isbn      = {978-0-262-03270-4},
  pages     = {I-XIV, 1-314},
  ee        = {http://books.google.de/books?id=Nmc4wEaLXFEC},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}

@inproceedings{DBLP:conf/birthday/BrijderER11,
  author    = {Robert Brijder and
               Andrzej Ehrenfeucht and
               Grzegorz Rozenberg},
  title     = {Reaction Systems with Duration},
  booktitle = {Computation, Cooperation, and Life},
  year      = {2011},
  pages     = {191-202},
  ee        = {http://dx.doi.org/10.1007/978-3-642-20000-7_16},
  crossref  = {DBLP:conf/birthday/2011paun},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}

@proceedings{DBLP:conf/birthday/2011paun,
  editor    = {Jozef Kelemen and
               Alica Kelemenov{\'a}},
  title     = {Computation, Cooperation, and Life - Essays Dedicated to
               Gheorghe Paun on the Occasion of His 60th Birthday},
  booktitle = {Computation, Cooperation, and Life},
  publisher = {Springer},
  series    = lncs,
  volume    = {6610},
  year      = {2011},
  isbn      = {978-3-642-19999-8},
  ee        = {http://dx.doi.org/10.1007/978-3-642-20000-7},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}

@InProceedings{timestamp,
 author = {Hans-Michael Hanisch and Kurt Lautenbach and Carlo Simon and Jan Thieme},
 title = {Timestamp Petri Nets in Technical Applications},
 booktitle = { WODES '98},
 pages = {321-326},
 year = {1998},
 }

 @InProceedings{koutnyreaction,
 author = {Jetty Kleijn and Maciej Koutny and Grzegorz Rozenberg},
 title = {Modelling Reaction Systems with Petri Nets},
 booktitle = {BioPPN-2011},
 pages = {36-52},
 year = {2011},
}

@article{DBLP:journals/nc/ChaouiyaNRT11,
  author    = {Claudine Chaouiya and
               Aur{\'e}lien Naldi and
               Elisabeth Remy and
               Denis Thieffry},
  title     = {Petri net representation of multi-valued logical regulatory
               graphs},
  journal   = {Natural Computing},
  volume    = {10},
  number    = {2},
  year      = {2011},
  pages     = {727-750},
  ee        = {http://dx.doi.org/10.1007/s11047-010-9178-0},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}


@article{DBLP:journals/fuin/KleijnK11,
  author    = {Jetty Kleijn and
               Maciej Koutny},
  title     = {Membrane Systems with Qualitative Evolution Rules},
  journal   = {Fundam. Inform.},
  volume    = {110},
  number    = {1-4},
  year      = {2011},
  pages     = {217-230},
  ee        = {http://dx.doi.org/10.3233/FI-2011-539},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}
 